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- PDB-2js7: Solution NMR structure of human myeloid differentiation primary r... -

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Basic information

Entry
Database: PDB / ID: 2js7
TitleSolution NMR structure of human myeloid differentiation primary response (MyD88). Northeast Structural Genomics target HR2869A
ComponentsMyeloid differentiation primary response protein MyD88
KeywordsSIGNALING PROTEIN / MYD88_HUMAN / TIR DOMAIN / TOLL LIKE RECEPTOR ADAPTOR DOMAIN / innate immune signaling / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / TIR domain binding ...regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / TIR domain binding / response to molecule of fungal origin / toll-like receptor 8 signaling pathway / positive regulation of lymphocyte proliferation / response to peptidoglycan / establishment of endothelial intestinal barrier / positive regulation of interleukin-23 production / IRAK4 deficiency (TLR5) / regulation of neutrophil migration / toll-like receptor TLR6:TLR2 signaling pathway / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / Toll-like receptor binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / interleukin-33-mediated signaling pathway / neutrophil activation involved in immune response / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / positive regulation of cytokine production involved in inflammatory response / death receptor binding / interleukin-1 receptor binding / MyD88 deficiency (TLR2/4) / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / 3'-UTR-mediated mRNA stabilization / toll-like receptor 4 signaling pathway / extrinsic component of plasma membrane / skin development / positive regulation of NLRP3 inflammasome complex assembly / type I interferon-mediated signaling pathway / defense response to protozoan / response to amine / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of interleukin-17 production / positive regulation of type I interferon production / response to amino acid / immunoglobulin mediated immune response / phagocytosis / signaling adaptor activity / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / response to interleukin-1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / response to organic cyclic compound / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / Interleukin-1 signaling / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / gene expression / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / molecular adaptor activity / cell surface receptor signaling pathway / endosome membrane / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / positive regulation of gene expression / apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Myeloid differentiation primary response protein MyD88 / MyD88, death domain / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance ...Myeloid differentiation primary response protein MyD88 / MyD88, death domain / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Death-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Myeloid differentiation primary response protein MyD88
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRossi, P. / Ramelot, T.A. / Tao, X. / Ciano, M. / Ho, C. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Kennedy, M.A. / Tong, L. ...Rossi, P. / Ramelot, T.A. / Tao, X. / Ciano, M. / Ho, C. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Kennedy, M.A. / Tong, L. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Human Myeloid Differentiation Primary Response (MyD88).
Authors: Rossi, P. / Xiao, R. / Tao, X. / Acton, T.B. / Tong, L. / Montelione, G.T.
History
DepositionJun 29, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Structure summary
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myeloid differentiation primary response protein MyD88


Theoretical massNumber of molelcules
Total (without water)18,7601
Polymers18,7601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Myeloid differentiation primary response protein MyD88


Mass: 18759.879 Da / Num. of mol.: 1 / Fragment: C-Terminal TIR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYD88 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q99836
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1232D 1H-13C HSQC
1333D HN(CA)CB
1433D HNCO
1533D HNCA
1633D HN(COCA)CB
1733D HN(CO)CA
1833D HN(CA)CO
1933D HBHA(CO)NH
11033D 1H-13C NOESY
11133D 1H-15N NOESY
11233D (H)CCH-COSY
11333D (H)CCH-TOCSY
11433D CCH-TOCSY
11512D 1H-13C HSQC stereospecific VL
11623D 1H-13C NOESY
11722D 1H-13C HSQC
1182H/D exch
1191HETnoe
1201T1/T2

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 100% D2O100% D2O
30.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity[U-5% 13C; U-100% 15N]1
10 mMDTT1
40 mMammonium acetate1
5 %acetonitrile1
0.8 mMentity[U-100% 13C; U-100% 15N]2
10 mMDTT2
40 mMammonium acetate2
5 %acetonitrile2
0.8 mMentity[U-100% 13C; U-100% 15N]3
10 mMDTT3
40 mMammonium acetate3
5 %acetonitrile3
Sample conditionspH: 5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
AutoAssign1.14Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky2.11Goddarddata analysis
NMRPipe2005Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin1.3Bruker Biospincollection
MOLMOL2K.2Koradi, Billeter and Wuthrichvisualization
PSVS1.3Bhattacharya and Montelionevalidation
ProcheckNMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thvalidation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
MolProbityRichardsonvalidation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR T1/T2. MEASURED TC = 12.1 +/- 1NS AT 20DEG. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS ...Details: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR T1/T2. MEASURED TC = 12.1 +/- 1NS AT 20DEG. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA AND AUTOSTRUCTURE IN A CONSENSUS APPROACH. SIMULATED ANNEALING MD LOWEST TARGET FUNCTION SELECTED WITH CYANA, LOWEST ENERGY SELECTED IN AUTOSTRUCTURE USING NIH-XPLOR FOR SIMULATEED ANNEALING MD. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 94.36%, SIDECHAIN 95.8%, AROMATIC (SC) 93.1%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2795 NOE. 100 STRUCTURES CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.35 A (1MODEL). 16 CLOSE CONTACTS TOTAL PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - ALPHA HELIX (28-39, 68-71, 81-85, 87-99, 103-106, 141-150), BETA-STRAND (48-49, 17-22, 72-78, 108-112, 130-131) [S(PHI)+ (PSI)] > 1.8. RMSD 0.6 BB, 0.9 ALL HEAVY ATOMS. RAMACHANDRAN: 88.0% MOST FAV, 11.4% ADDTL ALLOW, 0.5 GENEROUS ALLOW, 0.1% DISALLOW. PROCHECK (PSI-PHI): -0.22/-0.55 (RAW/Z), PROCHECK (ALL): -0.15/-0.89 (RAW/Z), MOLPROBITY CLASH: 27.22/-3.15 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.934, PRECISION: 0.892, F-MEASURE: 0.913, DP-SCORE: 0.721.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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